root.dir <- here::here()
knitr::opts_chunk$set(echo = TRUE, root.dir=root.dir)
knitr::opts_knit$set(root.dir = root.dir)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)
The data/haplotype_amino.fas from haplotype analysis is used for generating phylogeneitic tree of the haplotypes and assessing correlation between haplotypes. Trees were calculated using hamming distance method which calculates pairwise distance matrix for corresponding residues between sequences of equal lengths. Corelation between haplotypes is assessed using heatmaply
library(adegenet)
library(ips)
library(ggplot2)
library(ggtree)
library(heatmaply)
nbin<-fasta2DNAbin("data/haplotypes_AA_names.fas")
an<-as.alignment(nbin)
nm<-as.matrix(an)
nbinmat<-as.matrix(labels(nbin))
class(nbin)
dnbin<-dist.dna(nbin, model = "K80")
tree<-njs(dnbin)
ggt<-ggtree(tree, cex = 0.8, aes(color=branch.length))+scale_color_continuous(high='lightskyblue1',low='coral4')+geom_tiplab(align=TRUE, size=5)+geom_treescale(y = -1, color = "coral4", fontsize = 7)
njmsaplot<-msaplot(ggt, nbin, offset = 0.009, width=1, height = 0.5, color = c(rep("rosybrown", 1), rep("sienna1", 1), rep("lightgoldenrod1", 1), rep("lightskyblue1", 1)))
njmsaplot
pdf("figures/haplotype_tree.pdf", width = 11, height = 9, paper = "a4", pointsize=15)#save as pdf file
njmsaplot
dev.off()
sat2 <- NULL
for (i in 1:nrow(nm)) {
sat2[i] <- paste(nm[i, ], collapse="")
}
sat2 <- toupper(sat2)
sat3 <- unique(sat2)
comat = matrix(nrow=length(sat3), ncol=length(sat3))
for (i in 1:length(sat3)) {
si <- sat3[i]
for (j in 1:length(sat3)) {
sj <- sat3[j]
difcnt = 0
s1 = as.vector(strsplit(as.character(si), ""))
s2 = as.vector(strsplit(as.character(sj), ""))
for (k in 1:length(s1[[1]])) {
if (s1[[1]][k] != s2[[1]][k]) {
difcnt = difcnt + 1
}
comat[i, j] = difcnt
#print(paste(i, " ", j, " ", difcnt))
}
}
}
#comat is Hamming distance matrix
colnames(comat)<-nbinmat
heatmap<-heatmaply_cor(cor(comat), file= "figures/heatmap.pdf", xlab= "haplotypes", ylab="haplotypes",
k_col=3,
k_row=3, margins =c(10,10,15), fontsize_row = 8,
fontsize_col = 8)
heatmap
Figures are available haplotypes_trees and Haplotype_correlations